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Inputs for MultiBamExpressionQuantification
The following is an overview of all available inputs in MultiBamExpressionQuantification.
Required inputs
- MultiBamExpressionQuantification.bams
-
Array[Pair[String,struct(file : File, index : File, md5sum : String?)]]+
A list of pairs in which the left item is a sample Id and the right item an object containing the paths to that samples BAM file and its index. - MultiBamExpressionQuantification.strandedness
-
String
The strandedness of the RNA sequencing library preparation. One of "None" (unstranded), "FR" (forward-reverse: first read equal transcript) or "RF" (reverse-forward: second read equals transcript).
Other common inputs
- MultiBamExpressionQuantification.detectNovelTranscripts
-
Boolean — Default:
if defined(referenceGtfFile) then false else true
Whether or not a transcripts assembly should be used. If set to true Stringtie will be used to create a new GTF file based on the BAM files. This generated GTF file will be used for expression quantification. If `referenceGtfFile` is also provided this reference GTF will be used to guide the assembly. - MultiBamExpressionQuantification.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - MultiBamExpressionQuantification.referenceGtfFile
-
File?
A reference GTF file. If detectNovelTranscripts is set to true then this reference GTF will be used as a guide during transcript assembly, otherwise this GTF file is used directly as the annotation source for read counting. If undefined `detectNovelTranscripts` will be set to true by default. - MultiBamExpressionQuantification.stringtieAssembly.geneAbundanceFile
-
String?
Where the abundance file should be written.
Advanced inputs
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- MultiBamExpressionQuantification.additionalAttributes
-
Array[String]+?
Additional attributes which should be taken from the GTF used for quantification and added to the merged expression value tables. - MultiBamExpressionQuantification.dockerImages
-
Map[String,String] — Default:
{"htseq": "quay.io/biocontainers/htseq:0.11.2--py37h637b7d7_1", "stringtie": "quay.io/biocontainers/stringtie:1.3.4--py35_0", "collect-columns": "quay.io/biocontainers/collect-columns:0.2.0--py_1"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - MultiBamExpressionQuantification.htSeqCount.additionalAttributes
-
Array[String] — Default:
[]
Equivalent to the --additional-attr option of htseq-count. - MultiBamExpressionQuantification.htSeqCount.featureType
-
String?
Equivalent to the --type option of htseq-count. - MultiBamExpressionQuantification.htSeqCount.format
-
String — Default:
"bam"
Equivalent to the -f option of htseq-count. - MultiBamExpressionQuantification.htSeqCount.idattr
-
String?
Equivalent to the --idattr option of htseq-count. - MultiBamExpressionQuantification.htSeqCount.memory
-
String — Default:
"40G"
The amount of memory the job requires in GB. - MultiBamExpressionQuantification.htSeqCount.order
-
String — Default:
"pos"
Equivalent to the -r option of htseq-count. - MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.featureAttribute
-
String?
Equivalent to the -F option of collect-columns. - MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.featureColumn
-
Int?
Equivalent to the -f option of collect-columns. - MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.header
-
Boolean — Default:
false
Equivalent to the -H flag of collect-columns. - MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.separator
-
Int?
Equivalent to the -s option of collect-columns. - MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.valueColumn
-
Int?
Equivalent to the -c option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieFPKMs.featureAttribute
-
String?
Equivalent to the -F option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieFPKMs.featureColumn
-
Int?
Equivalent to the -f option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieFPKMs.separator
-
Int?
Equivalent to the -s option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieTPMs.featureAttribute
-
String?
Equivalent to the -F option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieTPMs.featureColumn
-
Int?
Equivalent to the -f option of collect-columns. - MultiBamExpressionQuantification.mergedStringtieTPMs.separator
-
Int?
Equivalent to the -s option of collect-columns. - MultiBamExpressionQuantification.mergeStringtieGtf.keepMergedTranscriptsWithRetainedIntrons
-
Boolean — Default:
false
Equivalent to the -i flag of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.label
-
String?
Equivalent to the -l option of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.memory
-
String — Default:
"10G"
The amount of memory needed for this task in GB. - MultiBamExpressionQuantification.mergeStringtieGtf.minimumCoverage
-
Float?
Equivalent to the -c option of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.minimumFPKM
-
Float?
Equivalent to the -F option of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.minimumIsoformFraction
-
Float?
Equivalent to the -f option of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.minimumLength
-
Int?
Equivalent to the -m option of 'stringtie --merge'. - MultiBamExpressionQuantification.mergeStringtieGtf.minimumTPM
-
Float?
Equivalent to the -T option of 'stringtie --merge'. - MultiBamExpressionQuantification.stringtie.memory
-
String — Default:
"10G"
The amount of memory needed for this task in GB. - MultiBamExpressionQuantification.stringtie.threads
-
Int — Default:
1
The number of threads to use. - MultiBamExpressionQuantification.stringtieAssembly.memory
-
String — Default:
"10G"
The amount of memory needed for this task in GB. - MultiBamExpressionQuantification.stringtieAssembly.threads
-
Int — Default:
1
The number of threads to use.